I receive emails like this at least twice a month: "I bred two black dogs and got a liver puppy. Is something wrong? Could there be a mistake?" The relief in people's voices when I explain what happened is almost palpable. Nothing is wrong. This is genetics working exactly as it should.
Hidden genetics explains the "impossible" puppies. The colors that appear out of nowhere. The ones that make you question your breeding records. Let me pull back the curtain.
The Carrier Problem
Remember from Color Genetics 101 that recessive traits need two copies to express. One copy? The trait hides. It is there, but you cannot see it.
A black dog with the genotype Bb looks exactly like a black dog with BB. Identical phenotypes. But one carries chocolate and one does not. Without DNA testing, you cannot tell them apart.
Now imagine breeding two Bb dogs. According to our Punnett square calculations, 25% of puppies will be bb. Chocolate puppies from two black parents. Surprise!
Except it is not really a surprise once you understand the mechanism. It is probability playing out exactly as predicted.
How Genes Hide for Generations
Here is where it gets interesting. A recessive gene can pass through multiple generations of carriers without ever appearing in a visible dog.
Let us trace a hypothetical chocolate gene through four generations:
- Generation 1: Grandpa is Bb (black, carries chocolate). Bred to a BB female.
- Generation 2: All puppies are either BB or Bb. All appear black. One Bb puppy is kept for breeding.
- Generation 3: That Bb dog is bred to another BB. Same results. A Bb puppy is kept.
- Generation 4: This time, the Bb dog is bred to another Bb (perhaps from a different line). Finally, a chocolate puppy appears.
The chocolate gene was present in every generation. Four generations of black dogs, then suddenly chocolate. The breeder who produced that chocolate might have no idea it was coming. Their records show black for generations back.
A Real Story
I worked with a Border Collie breeder who had bred only black and white dogs for twenty years. Then she acquired a new stud who was also black and white. Their first litter included a beautiful red puppy. She was convinced someone had made a mistake with the semen. DNA parentage testing confirmed both parents. What happened? Both dogs carried the recessive ee gene that produces red. Twenty years of black dogs, and the gene had been there all along in her lines, just never matched with another carrier.
The Multiple Gene Surprise
It gets more complex when multiple genes are involved. Remember from my loci guide that color is controlled by many genes working together.
Consider the lilac/isabella color, which requires homozygous recessive at BOTH B and D loci (bbdd).
For a lilac puppy to appear, it needs:
- Two copies of the chocolate gene (bb)
- Two copies of the dilute gene (dd)
Both parents must contribute both recessive alleles. If both parents are BbDd (black, carrying both chocolate and dilute), only 1 in 16 puppies will be lilac.
A breeder could produce dozens of litters from BbDd parents before a lilac appears. That is not bad luck. That is small sample sizes and low probability events.
The E Locus Mask
The E locus creates a particularly interesting form of hidden genetics. A dog that is ee (recessive red/yellow) cannot display any of its eumelanin genes in its coat.
A cream-colored dog could be carrying combinations at any of the major color loci:
- Black (B_) or chocolate (bb) at the B locus
- Full color (D_) or dilute (dd) at the D locus
- Any A locus combination
- Any K locus combination
You cannot tell any of this by looking at the dog. The E locus has masked it all. This is why Golden Retrievers, all ee, could theoretically carry genes for virtually any color pattern. They just cannot express them.
If you breed two ee dogs together, all puppies will be ee (cream/red/yellow). But they will inherit various hidden genes from their parents that could resurface in future generations if ever bred to dogs with normal extension.
Clearing vs Carriers: Strategic Breeding
Once you understand hidden genetics, you can breed strategically to either produce or avoid certain colors.
To clear a line of a hidden gene:
Breed suspected carriers to homozygous dominant dogs. If your dog is Bb (carries chocolate), breed to a confirmed BB dog. Half the puppies will be BB (cleared of the chocolate gene), half will be Bb (still carriers). Use Punnett square calculations to visualize these outcomes, then DNA test the puppies and keep the BB ones for breeding.
To produce a specific recessive color:
You need both parents to contribute the recessive allele. Breed a carrier to a carrier, or a carrier to an affected (homozygous recessive) dog, or two affected dogs together.
When to DNA Test
I used to tell breeders to test if they were "curious." Now I tell them to test if they want to breed predictably. Every hidden gene you identify is one less surprise in your litters. The cost of a color panel has dropped dramatically in recent years. It is the best investment a serious breeder can make. See my full guide on which DNA tests to run.
Why "Skip a Generation" Is Misleading
You have probably heard people say a trait "skipped a generation." This phrase drives geneticists a little bit crazy because it implies the gene was absent and then came back.
Genes do not skip anything. What actually happens is:
- A dog carries one copy of a recessive gene (is heterozygous)
- That dog passes the gene to some offspring, who also carry it
- Those carriers pass it to their offspring
- Eventually, two carriers are bred together
- Some of their puppies receive two copies and express the trait
The gene was present in every generation. It never "skipped" anywhere. It was just hidden, waiting for two carriers to meet.
Case Study: The Unexpected Blue
Let me share a detailed case that illustrates these principles perfectly.
A breeder contacted me because her litter of Staffordshire Bull Terriers included a blue puppy. Both parents were black, from lines that had produced only black for as long as anyone could remember. She wanted to know if the blue puppy could actually be from this breeding.
We ran DNA tests on both parents. Results:
- Sire: B/B D/d (Black, carries dilute)
- Dam: B/B D/d (Black, carries dilute)
Mystery solved. Both parents carried one copy of the dilute gene. When both passed that dilute copy to the same puppy, the result was blue (B/B d/d).
The dilute gene had been present in both lines, passed down through generations of black dogs who each carried one hidden copy. The odds of getting a blue puppy from two D/d parents is 25%. Perfectly normal. Perfectly predictable. Just not predicted because nobody knew to test for it.
Prevention Through Testing
If you want to avoid surprise colors, the solution is simple: test your breeding dogs for all relevant color genes before breeding.
A comprehensive color panel will reveal:
- What your dog looks like (you already know this)
- What recessive genes your dog carries (you cannot know without testing)
With that information, you can predict litter outcomes using Punnett squares. No more surprises. No more wondering if the semen got mixed up or if the paperwork is wrong.
Embracing the Surprise
I should note that not all breeders want to eliminate surprise colors. Some love the variety that hidden genetics provides. There is something magical about a litter where you genuinely do not know what colors will emerge.
Both approaches are valid. The key is understanding what is happening genetically so you can make informed decisions. Surprise by choice is different from surprise by ignorance.
What To Do When Surprise Happens
If you get an unexpected color in a litter:
- Do not panic. It is almost certainly genetics, not a mistake.
- Consider parentage testing if you need official confirmation.
- DNA test the puppy to learn its exact genotype.
- Test the parents to understand what they carry.
- Update your records with the new genetic information.
- Use this knowledge for future breeding decisions.
Every surprise puppy is an opportunity to learn something about your lines. Do not waste it.
For detailed information on DNA testing options and interpretation, read my guide on which color DNA tests to run and why.
Hidden Genes Beyond Color
The same principles that apply to hidden color genes apply to hidden health genes. Recessive health conditions can lurk in lines for generations before appearing. For herding breeds specifically, learn about inherited conditions at The Herding Gene.